Accurately modelling cold and ultracold reactive collisions occurring over deep potential wells, such as D⁺ + H₂ → H⁺ + HD, requires the development of new theoretical and computational ...methodologies. One potentially useful framework is the R-matrix method adopted widely for electron–molecule collisions which has more recently been applied to non-reactive heavy-particle collisions such as Ar–Ar. The existing treatment of non-reactive elastic and inelastic scattering needs to be substantially extended to enable modelling of reactive collisions: this is the subject of this paper. Herein, we develop the general mathematical formulation for non-reactive elastic and inelastic scattering, photoassociation, photodissociation, charge exchange and reactive scattering using the R-matrix method. Of particular note is that the inner region, of central importance to calculable R-matrix methodologies, must be finite in all scattering coordinates rather than a single scattering coordinate as for non-reactive scattering.
This article is part of a discussion meeting issue ʻAdvances in hydrogen molecular ions:
H
3
+
,
H
5
+
and beyond’.
Why is the H 3 + hot spot above Jupiter’s Great Red Spot so hot? Ray, L. C.; Lorch, C. T. S.; O’Donoghue, J. ...
Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences,
09/2019, Volume:
377, Issue:
2154
Journal Article
Peer reviewed
Recent observations of Jupiter’s Great Red Spot indicate that the thermosphere above the storm is hotter than its surroundings by more than 700 K. Possible suggested sources for this heating have ...thus far included atmospheric gravity waves and lightning-driven acoustic waves. Here, we propose that Joule heating, driven by Great Red Spot vorticity penetrating up into the lower stratosphere and coupling to the thermosphere, may contribute to the large observed temperatures. The strength of Joule heating will depend on the local inclination angle of the magnetic field and thus the observed emissions and inferred temperatures should vary with planetary longitude as the Great Red Spot tracks across the planet.
This article is part of a discussion meeting issue ‘Advances in hydrogen molecular ions:
H
3
+
,
H
5
+
and beyond’.
Dissociative recombination of H 3 + and D 5 Larsson, Mats
Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences,
09/2019, Volume:
377, Issue:
2154
Journal Article
Peer reviewed
Compared with earlier years, the dissociative recombination of
H
3
+
has not been very actively studied in recent years. New results from afterglow experiments are quoted and compared with results ...from ion storage rings and theory. New results for
D
5
+
are discussed. This article also contains some historical remarks on hydrogen and its importance for the advancement of physics and chemistry.
This article is part of a discussion meeting issue ʻAdvances in hydrogen molecular ions:
H
3
+
,
H
5
+
and beyond’.
Non-adiabatic effects in the H 3 + spectrum Amaral, Paulo H. R.; Stanke, Monika; Adamowicz, Ludwik ...
Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences,
09/2019, Volume:
377, Issue:
2154
Journal Article
Peer reviewed
The effect of non-adiabatic coupling on the computed rovibrational energy levels amounts to about 2 cm−1 for
H
3
+
and must be included in high-accuracy calculations. Different strategies to obtain ...the corresponding energy shifts are reviewed in the article. A promising way is to introduce effective vibrational reduced masses that depend on the nuclear configuration. A new empirical method that uses the stockholder atoms-in-molecules approach to this effect is presented and applied to
H
3
+
. Furthermore, a highly accurate potential energy surface for the
D
3
+
isotopologue, which includes relativistic and leading quantum electrodynamic terms, is constructed and used to analyse the observed rovibrational frequencies for this molecule. Accurate band origins are obtained that improve existing data.
This article is part of a discussion meeting issue ʻAdvances in hydrogen molecular ions:
H
3
+
,
H
5
+
and beyond’.
Modelling H 3 + in planetary atmospheres Moore, L.; Melin, H.; O’Donoghue, J. ...
Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences,
09/2019, Volume:
377, Issue:
2154
Journal Article
Peer reviewed
Since its detection in the aurorae of Jupiter approximately 30 years ago, the
H
3
+
ion has served as an invaluable probe of giant planet upper atmospheres. However, the vast majority of monitoring ...of planetary
H
3
+
radiation has followed from observations that rely on deriving parameters from column-integrated paths through the emitting layer. Here, we investigate the effects of density and temperature gradients along such paths on the measured
H
3
+
spectrum and its resulting interpretation. In a non-isothermal atmosphere,
H
3
+
column densities retrieved from such observations are found to represent a lower limit, reduced by 20% or more from the true atmospheric value. Global simulations of Uranus’ ionosphere reveal that measured
H
3
+
temperature variations are often attributable to well-understood solar zenith angle effects rather than indications of real atmospheric variability. Finally, based on these insights, a preliminary method of deriving vertical temperature structure is demonstrated at Jupiter using model reproductions of electron density and
H
3
+
measurements. The sheer diversity and uncertainty of conditions in planetary atmospheres prohibits this work from providing blanket quantitative correction factors; nonetheless, we illustrate a few simple ways in which the already formidable utility of
H
3
+
observations in understanding planetary atmospheres can be enhanced.
This article is part of a discussion meeting issue ‘Advances in hydrogen molecular ions:
H
3
+
,
H
5
+
and beyond’.
Phenology is a key biological trait that can determine an organism's survival and provides one of the clearest indicators of the effects of recent climatic change. Long time-series observations of ...plant phenology collected at continental scales could clarify latitudinal and regional patterns of plant responses and illuminate drivers of that variation, but few such datasets exist. Here, we use the web tool CrowdCurio to crowdsource phenological data from over 7000 herbarium specimens representing 30 diverse flowering plant species distributed across the eastern United States. Our results, spanning 120 years and generated from over 2000 crowdsourcers, illustrate numerous aspects of continental-scale plant reproductive phenology. First, they support prior studies that found plant reproductive phenology significantly advances in response to warming, especially for early-flowering species. Second, they reveal that fruiting in populations from warmer, lower latitudes is significantly more phenologically sensitive to temperature than that for populations from colder, higher-latitude regions. Last, we found that variation in phenological sensitivities to climate within species between regions was of similar magnitude to variation between species. Overall, our results suggest that phenological responses to anthropogenic climate change will be heterogeneous within communities and across regions, with large amounts of regional variability driven by local adaptation, phenotypic plasticity and differences in species assemblages. As millions of imaged herbarium specimens become available online, they will play an increasingly critical role in revealing large-scale patterns within assemblages and across continents that ultimately can improve forecasts of the impacts of climatic change on the structure and function of ecosystems.
This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Functional traits are increasingly used to understand the ecology of plants and to predict their responses to global changes. Unfortunately, trait data are unavailable for the majority of plant ...species. The lack of trait data is especially prevalent for hard-to-measure traits and for tropical plant species, potentially owing to the many inherent difficulties of working with species in remote, hyperdiverse rainforest systems. The living collections of botanic gardens provide convenient access to large numbers of tropical plant species and can potentially be used to quickly augment trait databases and advance our understanding of species' responses to climate change. In this review, we quantitatively assess the availability of trait data for tropical versus temperate species, the diversity of species available for sampling in several exemplar tropical botanic gardens and the validity of garden-based leaf and root trait measurements. Our analyses support the contention that the living collections of botanic gardens are a valuable scientific resource that can contribute significantly to research on plant functional ecology and conservation.
This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 ...years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.
This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Facets of phylodiversity Kling, Matthew M.; Mishler, Brent D.; Thornhill, Andrew H. ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
01/2019, Volume:
374, Issue:
1763
Journal Article
Peer reviewed
Biodiversity is often described as having multiple facets, including species richness, functional diversity and phylogenetic diversity. In this paper, we argue that phylogenetic diversity itself has ...three distinct facets—lineage diversification, character divergence and survival time—that can be quantified using distinct branch length metrics on an evolutionary tree. Each dimension is related to different processes of macroevolution, has different spatial patterns and is tied to distinct goals for conserving biodiversity and protecting its future resilience and evolutionary potential. We compared the landscapes identified as top conservation priorities by each of these three metrics in a conservation gap analysis for California, a world biodiversity hotspot, using herbarium data on the biogeography and evolutionary relationships of more than 5000 native plant species. Our analysis incorporated a novel continuous metric of current land protection status, fine-scale data on landscape intactness and an optimization algorithm used to identify complementary priority sites containing concentrations of taxa that are evolutionarily unique, vulnerable due to small range size and/or poorly protected across their ranges. Top conservation priorities included pockets of coastal and northern California that ranked highly for all three phylodiversity dimensions and for species richness, as well as sites uniquely identified by each metric whose value may depend on whether properties such as genetic divergence, high net diversification or independent survival experience are most desirable in an Anthropocene flora.
This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Fossil Atmospheres Soul, Laura C.; Barclay, Richard S.; Bolton, Amy ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
01/2019, Volume:
374, Issue:
1763
Journal Article
Peer reviewed
Palaeontologists increasingly use large datasets of observations collected from museum specimens to address broad-scale questions about evolution and ecology on geological timescales. One such ...question is whether information from fossil organisms can be used as a robust proxy for atmospheric carbon dioxide through time. Here, we present the citizen science branch of 'Fossil Atmospheres', a project designed to refine stomatal index of Ginkgo leaves as a palaeo-CO2 proxy by involving citizen scientists in data collection through the Zooniverse website. Citizen science helped to overcome a barrier presented by the time taken to count cells in Ginkgo samples; however, a new set of challenges arose as a result. A beta-testing phase with Zooniverse volunteers provided an opportunity to improve instructions to ensure high fidelity data. Exploration of citizen scientists' estimates shows that volunteer counts of stomata are accurate with respect to counts made by the project's lead scientist. However, counts of epidermal cells have a wide range, and mean values tend to underestimate expert counts. We demonstrate a variety of approaches to reducing the inaccuracy in the calculated stomatal index that this variation causes. Zooniverse serves as an ideal tool for collection of palaeontological data where the distribution of fossils would be impossible, but where specimens can be easily imaged. Such an approach facilitates the collection of a large palaeontological dataset, as well as providing an opportunity for citizens to engage with climate research.
This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
